Transcriptional profiling of the developing murine intestine

To identify transcriptional changes during the development of the small intestine, we performed scRNAseq using MULTI-seq on 86,845 cells collected from embryos at E13.5-E18.5. We additionally identified transcriptional changes along the proximal-distal axis of the small intestine by isolating RNA from 2.5mm fragments of the tissue that had been cut along this axis. Mice were collected from Pdgfra-H2BGFP mice to enrich for mesenchymal populations. Single-cell RNA sequencing was performed using MULTI-seq on mouse embryonic intestinal tissues from Pdgfra-H2BGFP mice across five developmental time points with pooled replicates (E13.5, 4 replicates; E14.5, 3 replicates; E15.5, 2 replicates; E16.5, 2 replicates; and E18.5, 2 replicates). The intestines were divided into 2.5mm-length pieces along its proximal-distal axis (E13.5, 3 segments; E14.5, 5 segments; E15.5, 10 segments; E16.5, 15 segments; E18.5, 20 segments). We enriched for rare cell populations (PdgfraHigh, or Epcam+, or CD31+ or CD45+).